https://github.com/danielhiversen/neuroimageregistration

Registration of medical MR brain images to a common mr brain
https://github.com/danielhiversen/neuroimageregistration

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Registration of medical MR brain images to a common mr brain

• Host: GitHub
• URL: https://github.com/danielhiversen/neuroimageregistration
• Owner: Danielhiversen
• License: mit
• Created: 2016-02-08T12:45:44.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2020-10-24T10:41:17.000Z (about 4 years ago)
• Last Synced: 2024-06-13T08:44:17.496Z (7 months ago)
• Language: Python
• Homepage:
• Size: 421 KB
• Stars: 10
• Watchers: 3
• Forks: 7
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: License.txt

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README

        
# NeuroImageRegistration [![Build Status](https://travis-ci.org/Danielhiversen/NeuroImageRegistration.svg?branch=master)](https://travis-ci.org/Danielhiversen/NeuroImageRegistration)

## Install

http://neuro.debian.net/install_pkg.html?p=fsl-complete

sudo apt-get install -y libblas-dev liblapack-dev libfreetype6-dev

sudo apt-get install -y cmake ninja-build git

sudo apt-get install gfortran

git clone git://github.com/stnava/ANTs.git

mkdir antsbin

cd antsbin

cmake -G "Ninja" -DCMAKE_BUILD_TYPE=Release ../ANTs/

ninja

sudo apt-get install python-pip

cd

git clone [email protected]:Danielhiversen/NeuroImageRegistration.git

cd NeuroImageRegistration/

virtualenv venv

source venv/bin/activate

sudo pip install --upgrade setuptools

sudo pip install --upgrade distribute

pip install -r requirements.txt

ant registration parameters inspired by

http://miykael.github.io/nipype-beginner-s-guide/normalize.html

https://apps.icts.uiowa.edu/confluence/display/BRAINSPUBLIC/ANTS+conversion+to+antsRegistration+for+same+data+set

## Usage

Some computer specific pathes must be sat in util.py

ConvertDataToDB.py, ConvertDataToDB_menigiomer.py and ConvertDataToDB_MM.py are used to convert the data and add it to a database

do_img_registration.py,	

do_img_registration_GBM.py, 

do_img_registration_LGG_POST.py,	

do_img_registration_LGG_PRE.py	and 

do_img_registration_MM.py

are used do registration of the volume to a reference volume.

run_neuro_reg.sh, 

run_neuro_reg_gbm.sh, 

run_neuro_reg_gbm2.sh, 

run_neuro_reg_gbm3.sh and 

run_neuro_reg_gbm_post.sh

are used to do the image registration on a super computer 

postProcess.py,	

postProcess_GBM.py and 

postProcess_MM.py

are used post processing and generating figures